Yeah, it's important to use a decrypted ROM. Encrypted ones aren't supported, and because of legal concerns, I have no plans to add support.
I believe I've fixed the issue in the latest version. Please try again with this one.
I don't know for sure if it will resolve the crash, but the latest build did fix a crucial bug, and I think it's worth a try. Alternatively, the version Wol38 linked to may work.

I've never tested that but I think there wouldn't be trouble since it's an "evolution"
btw I saw that if you make evolve a Pokemon into the same Pokemon unchanged, it become temporarly white until the end of the scene ( a battle for exemple )

Depends on your choice on the evolved Pokemon, for me I chose Mega Manectric for base and for evolution, so he won't change.
Another thing is when you get petrified by Nuzleaf, you can see the base Pokemon as a stone statue (exemple Charmander), not the Pokemon that you have but it doesn't matter since you keep the modified Pokemon.